Combine output of metagenomic samples analyzed by bracken.
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
List of output files from bracken
*
Output
name:type
description
pattern
txt{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.txt{:bash}
:file
Combined output in table format
*.txt
versions_combine_bracken_outputs{:bash}
${task.process}{:bash}
:string
The name of the process
combine_bracken_outputs{:bash}
:string
The name of the tool
bracken -v | cut -f2 -d"v"{:bash}
:string
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions{:bash}
${task.process}{:bash}
:string
The name of the process
combine_bracken_outputs{:bash}
:string
The name of the tool
bracken -v | cut -f2 -d"v"{:bash}
:string
The expression to obtain the version of the tool
Tools
bracken
GPL v3
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
